public void testEnhanceDefer() throws IOException {
NetcdfDataset ncd =
NetcdfDataset.openDataset(
filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissing), -1, null, null);
VariableDS enhancedVar = (VariableDS) ncd.findVariable("t1");
NetcdfDataset ncdefer =
NetcdfDataset.openDataset(
filename, EnumSet.of(NetcdfDataset.Enhance.ScaleMissingDefer), -1, null, null);
VariableDS deferVar = (VariableDS) ncdefer.findVariable("t1");
Array data = enhancedVar.read();
Array dataDefer = deferVar.read();
System.out.printf("Enhanced=");
NCdumpW.printArray(data);
System.out.printf("%nDeferred=");
NCdumpW.printArray(dataDefer);
System.out.printf("%nProcessed=");
CompareNetcdf2 nc = new CompareNetcdf2(new Formatter(System.out), false, false, true);
assert !nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);
IndexIterator ii = dataDefer.getIndexIterator();
while (ii.hasNext()) {
double val = deferVar.convertScaleOffsetMissing(ii.getDoubleNext());
ii.setDoubleCurrent(val);
}
NCdumpW.printArray(dataDefer);
assert nc.compareData(enhancedVar.getShortName(), data, dataDefer, false);
ncd.close();
ncdefer.close();
}
// @todo Make sure units are meters
public Array getElevation(Range range) throws IOException, InvalidRangeException {
List section = new ArrayList(1);
section.add(range);
Array a = elevVar.read(section);
if (elevVarUnitsConversionFactor == 1.0) return (a);
for (IndexIterator it = a.getIndexIterator(); it.hasNext(); ) {
if (elevVar.getDataType() == DataType.DOUBLE) {
double val = it.getDoubleNext();
it.setDoubleCurrent(val * elevVarUnitsConversionFactor);
} else if (elevVar.getDataType() == DataType.FLOAT) {
float val = it.getFloatNext();
it.setFloatCurrent((float) (val * elevVarUnitsConversionFactor));
} else if (elevVar.getDataType() == DataType.INT) {
int val = it.getIntNext();
it.setIntCurrent((int) (val * elevVarUnitsConversionFactor));
} else if (elevVar.getDataType() == DataType.LONG) {
long val = it.getLongNext();
it.setLongCurrent((long) (val * elevVarUnitsConversionFactor));
} else {
throw new IllegalStateException(
"Elevation variable type <"
+ elevVar.getDataType().toString()
+ "> not double, float, int, or long.");
}
}
return (a);
}
// get a list of station obs for this station
public List getData(Station s, CancelTask cancel) throws IOException {
ArrayStructure stationData = readData("ID " + s.getName(), cancel);
ArrayList stationObs = new ArrayList();
IndexIterator ii = stationData.getIndexIterator();
while (ii.hasNext()) {
stationObs.add(new StationObs((Station) s, (StructureData) ii.getObjectNext()));
}
return stationObs;
}
// for jon blower
private Array getEnhancedArray(VariableDS vds) throws IOException {
Array data = vds.read();
EnumSet<NetcdfDataset.Enhance> mode = vds.getEnhanceMode();
if (mode.contains(NetcdfDataset.Enhance.ScaleMissing)) return data;
if (!mode.contains(NetcdfDataset.Enhance.ScaleMissingDefer))
throw new IllegalStateException("Must include " + NetcdfDataset.Enhance.ScaleMissingDefer);
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext()) {
double val = vds.convertScaleOffsetMissing(ii.getDoubleNext());
ii.setDoubleCurrent(val);
}
return data;
}
/**
* Get the minimum and the maximum data value of the previously read Array, skipping missing
* values as defined by isMissingData(double val).
*
* @param a Array to get min/max values
* @return both min and max value.
*/
public MAMath.MinMax getMinMaxSkipMissingData(Array a) {
if (!hasMissingData()) return MAMath.getMinMax(a);
IndexIterator iter = a.getIndexIterator();
double max = -Double.MAX_VALUE;
double min = Double.MAX_VALUE;
while (iter.hasNext()) {
double val = iter.getDoubleNext();
if (isMissingData(val)) continue;
if (val > max) max = val;
if (val < min) min = val;
}
return new MAMath.MinMax(min, max);
}
private void readOneRadial(Cinrad2Record r, int datatype, Range gateRange, IndexIterator ii)
throws IOException {
if (r == null) {
for (int i = gateRange.first(); i <= gateRange.last(); i += gateRange.stride())
ii.setByteNext(Cinrad2Record.MISSING_DATA);
return;
}
r.readData(volScan.raf, datatype, gateRange, ii);
}
private void showValuesAsDates(CoordinateAxis axis) {
String units = axis.getUnitsString();
String cal = getCalendarAttribute(axis);
CalendarDateUnit cdu = CalendarDateUnit.of(cal, units);
try {
infoTA.appendLine(units);
infoTA.appendLine(NCdumpW.printVariableData(axis, null));
if (axis.getDataType().isNumeric()) {
if (axis instanceof CoordinateAxis2D) {
showDates2D((CoordinateAxis2D) axis, cdu);
} else if (axis instanceof CoordinateAxis1D) { // 1D
showDates1D((CoordinateAxis1D) axis, cdu);
} else { // > 2D
Array data = axis.read();
IndexIterator ii = data.getIndexIterator();
while (ii.hasNext()) {
double val = ii.getDoubleNext();
infoTA.appendLine(makeCalendarDateStringOrMissing(cdu, val));
}
}
} else { // must be iso dates
Array data = axis.read();
Formatter f = new Formatter();
if (data instanceof ArrayChar) {
ArrayChar dataS = (ArrayChar) data;
ArrayChar.StringIterator iter = dataS.getStringIterator();
while (iter.hasNext()) f.format(" %s%n", iter.next());
infoTA.appendLine(f.toString());
} else if (data instanceof ArrayObject) {
IndexIterator iter = data.getIndexIterator();
while (iter.hasNext()) f.format(" %s%n", iter.next());
infoTA.appendLine(f.toString());
}
}
} catch (Exception ex) {
ex.printStackTrace();
infoTA.appendLine(ex.getMessage());
}
}
private void showDates2D(CoordinateAxis2D axis2D, CalendarDateUnit cdu) {
Formatter f = new Formatter();
if (axis2D.isInterval()) {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
ArrayDouble.D3 bounds = axis2D.getCoordBoundsArray();
if (bounds == null) {
infoTA.appendLine("No bounds for interval " + axis2D.getFullName());
return;
}
IndexIterator coordIter = coords.getIndexIterator();
IndexIterator boundsIter = bounds.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds1 = boundsIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds2 = boundsIter.getDoubleNext();
f.format(
"%s (%s,%s)%n",
makeCalendarDateStringOrMissing(cdu, coordValue),
makeCalendarDateStringOrMissing(cdu, bounds1),
makeCalendarDateStringOrMissing(cdu, bounds2));
}
} else {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
IndexIterator coordIter = coords.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
f.format("%s%n", makeCalendarDateStringOrMissing(cdu, coordValue));
}
}
infoTA.appendLine(f.toString());
}
private void showValues2D(CoordinateAxis2D axis2D) {
Formatter f = new Formatter();
if (axis2D.isInterval()) {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
ArrayDouble.D3 bounds = axis2D.getCoordBoundsArray();
if (bounds == null) {
infoTA.appendLine("No bounds for interval " + axis2D.getFullName());
return;
}
IndexIterator coordIter = coords.getIndexIterator();
IndexIterator boundsIter = bounds.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds1 = boundsIter.getDoubleNext();
if (!boundsIter.hasNext()) break;
double bounds2 = boundsIter.getDoubleNext();
f.format("%f (%f,%f) = %f%n", coordValue, bounds1, bounds2, bounds2 - bounds1);
}
} else {
ArrayDouble.D2 coords = axis2D.getCoordValuesArray();
IndexIterator coordIter = coords.getIndexIterator();
while (coordIter.hasNext()) {
double coordValue = coordIter.getDoubleNext();
f.format("%f%n", coordValue);
}
}
infoTA.appendLine(f.toString());
}
private void makeCoordinateDataWithMissing(
int datatype,
Variable time,
Variable elev,
Variable azi,
Variable nradialsVar,
Variable ngatesVar,
List groups) {
Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
Index timeIndex = timeData.getIndex();
Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
Index elevIndex = elevData.getIndex();
Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
Index aziIndex = aziData.getIndex();
Array nradialsData =
Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
IndexIterator nradialsIter = nradialsData.getIndexIterator();
Array ngatesData =
Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
IndexIterator ngatesIter = ngatesData.getIndexIterator();
// first fill with missing data
IndexIterator ii = timeData.getIndexIterator();
while (ii.hasNext()) ii.setIntNext(MISSING_INT);
ii = elevData.getIndexIterator();
while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);
ii = aziData.getIndexIterator();
while (ii.hasNext()) ii.setFloatNext(MISSING_FLOAT);
// now set the coordinate variables from the Cinrad2Record radial
int last_msecs = Integer.MIN_VALUE;
int nscans = groups.size();
try {
for (int scan = 0; scan < nscans; scan++) {
List scanGroup = (List) groups.get(scan);
int nradials = scanGroup.size();
Cinrad2Record first = null;
for (int j = 0; j < nradials; j++) {
Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
if (first == null) first = r;
int radial = r.radial_num - 1;
timeData.setInt(timeIndex.set(scan, radial), r.data_msecs);
elevData.setFloat(elevIndex.set(scan, radial), r.getElevation());
aziData.setFloat(aziIndex.set(scan, radial), r.getAzimuth());
if (r.data_msecs < last_msecs)
logger.warn("makeCoordinateData time out of order " + r.data_msecs);
last_msecs = r.data_msecs;
}
nradialsIter.setIntNext(nradials);
ngatesIter.setIntNext(first.getGateCount(datatype));
}
} catch (java.lang.ArrayIndexOutOfBoundsException ae) {
logger.debug("Cinrad2IOSP.uncompress ", ae);
}
time.setCachedData(timeData, false);
elev.setCachedData(elevData, false);
azi.setCachedData(aziData, false);
nradialsVar.setCachedData(nradialsData, false);
ngatesVar.setCachedData(ngatesData, false);
}
private void makeCoordinateData(
int datatype,
Variable time,
Variable elev,
Variable azi,
Variable nradialsVar,
Variable ngatesVar,
List groups) {
Array timeData = Array.factory(time.getDataType().getPrimitiveClassType(), time.getShape());
IndexIterator timeDataIter = timeData.getIndexIterator();
Array elevData = Array.factory(elev.getDataType().getPrimitiveClassType(), elev.getShape());
IndexIterator elevDataIter = elevData.getIndexIterator();
Array aziData = Array.factory(azi.getDataType().getPrimitiveClassType(), azi.getShape());
IndexIterator aziDataIter = aziData.getIndexIterator();
Array nradialsData =
Array.factory(nradialsVar.getDataType().getPrimitiveClassType(), nradialsVar.getShape());
IndexIterator nradialsIter = nradialsData.getIndexIterator();
Array ngatesData =
Array.factory(ngatesVar.getDataType().getPrimitiveClassType(), ngatesVar.getShape());
IndexIterator ngatesIter = ngatesData.getIndexIterator();
int last_msecs = Integer.MIN_VALUE;
int nscans = groups.size();
int maxRadials = volScan.getMaxRadials();
for (int i = 0; i < nscans; i++) {
List scanGroup = (List) groups.get(i);
int nradials = scanGroup.size();
Cinrad2Record first = null;
for (int j = 0; j < nradials; j++) {
Cinrad2Record r = (Cinrad2Record) scanGroup.get(j);
if (first == null) first = r;
timeDataIter.setIntNext(r.data_msecs);
elevDataIter.setFloatNext(r.getElevation());
aziDataIter.setFloatNext(r.getAzimuth());
if (r.data_msecs < last_msecs)
logger.warn("makeCoordinateData time out of order " + r.data_msecs);
last_msecs = r.data_msecs;
}
for (int j = nradials; j < maxRadials; j++) {
timeDataIter.setIntNext(MISSING_INT);
elevDataIter.setFloatNext(MISSING_FLOAT);
aziDataIter.setFloatNext(MISSING_FLOAT);
}
nradialsIter.setIntNext(nradials);
ngatesIter.setIntNext(first.getGateCount(datatype));
}
time.setCachedData(timeData, false);
elev.setCachedData(elevData, false);
azi.setCachedData(aziData, false);
nradialsVar.setCachedData(nradialsData, false);
ngatesVar.setCachedData(ngatesData, false);
}